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- PDB-3nq1: Crystal Structure of Tyrosinase from Bacillus megaterium in compl... -

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Basic information

Entry
Database: PDB / ID: 3nq1
TitleCrystal Structure of Tyrosinase from Bacillus megaterium in complex with inhibitor kojic acid
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / tyrosinase / type3 copper proteins / Bacillus megaterium / oxidoreductase / kojic acid / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


tyrosinase activity / melanin biosynthetic process / pigmentation / metal ion binding
Similarity search - Function
di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / 5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE / Tyrosinase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSendovski, M. / Kanteev, M. / Adir, N. / Fishman, A.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: First structures of an active bacterial tyrosinase reveal copper plasticity.
Authors: Sendovski, M. / Kanteev, M. / Shuster Ben-Yosef, V. / Adir, N. / Fishman, A.
#1: Journal: To be Published
Title: Crystallization and preliminary x-ray crystallographic analysis of a bacterial tyrosinase from Bacillus megaterium
Authors: Sendovski, M. / Kanteev, M. / Adir, N. / Fishman, A.
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosinase
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,95821
Polymers70,5692
Non-polymers1,38919
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-395 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.380, 83.530, 146.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosinase


Mass: 35284.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2ZB02, tyrosinase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-KOJ / 5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE


Mass: 142.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG 8000, zinc acetate, sodium cacodylate, pH 6.1, vapor diffusion, hanging drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→73.08 Å / Num. all: 28766 / Num. obs: 24154 / % possible obs: 84.7 % / Redundancy: 2.2 % / Rsym value: 0.088 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.3-2.421.90.2922.40.292172.8
2.42-2.572.10.2432.80.243187
2.57-2.752.20.1913.60.191189.1
2.75-2.972.20.1444.60.144188.3
2.97-3.252.20.0986.60.098187.8
3.25-3.642.20.06210.90.062186.3
3.64-4.22.30.04411.80.044185.8
4.2-5.142.30.03518.20.035185.1
5.14-7.272.30.04214.60.042183.6
7.27-48.722.20.03414.90.034180.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.16 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å43.76 Å
Translation3.5 Å43.76 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
PHENIX1.6.1_357refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.085 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 0.05 / Phase error: 28.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2939 1167 5.26 %
Rwork0.2599 --
obs0.2617 22178 77.14 %
all-28766 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.045 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2438 Å20 Å2-0 Å2
2--10.4766 Å2-0 Å2
3----9.0528 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å / Luzzati sigma a obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 37 206 4885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0224839
X-RAY DIFFRACTIONf_angle_d1.5286600
X-RAY DIFFRACTIONf_dihedral_angle_d16.2531762
X-RAY DIFFRACTIONf_chiral_restr0.098652
X-RAY DIFFRACTIONf_plane_restr0.009872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40470.39111130.34471961X-RAY DIFFRACTION59
2.4047-2.53150.38411650.33912387X-RAY DIFFRACTION72
2.5315-2.69010.36511400.31582602X-RAY DIFFRACTION77
2.6901-2.89770.32891400.30212723X-RAY DIFFRACTION81
2.8977-3.18920.3391490.27352773X-RAY DIFFRACTION82
3.1892-3.65050.2821540.23822801X-RAY DIFFRACTION82
3.6505-4.59830.1941530.19222852X-RAY DIFFRACTION83
4.5983-42.09160.22851530.21832912X-RAY DIFFRACTION81
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4koj.param

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